Digital Twins and Reproducibility

Bridging Point-and-Click COPASI Software with Open-Source and Flexible R Programming language

First Published: Mar 14, 2025

Last updated: May 16, 2025

Bastien CHASSAGNOL |
Post-Doc
LPSM and Laval

Lilija Wehling |
Ph.D.
VPE BioMed X Institute

Atreyee Banerjee |
Ph.D.
Mainz Universität

Soria Gasparini |
Ph.D.
Heidelberg University

Sanjana Balaji Kuttae |
Computational Biologist (Research Assistant)
VPE BioMed X Institute


Slides available on GitHub

Talks’ Layout

  • Reproducibility Crisis. 👋
  • IBD ODE Model 🕘
  • IBD Numerical Simulations 🕘
  • BioModels database ⬇️

Reproducibility Crisis

Cell-cell Categories

Classes of cell-cell communications cover:

CCC tools.

Main categories of cell communication. Reproduced from Fig1, Deciphering cell–cell interactions and communication from gene expression, from (armingol2021nrg?).


  • Autocrine signalling: induce a cellular response within the same cell.

  • Paracrine signalling: diffusion of signalling, secreted molecules in the external medium.

  • Juxtacrine signalling: contact-dependant, through gap junctions or membrane nanotubes.

  • Endocrine signalling: long-range intercellular communication enabled by blood-circulating hormones.

An ODE of the Immune System

Main categories of cell-cell tools

Phylogenetic tree of cell-cell tools

Phylogenetic tree of computational tools for inferring cell–cell interactions, from (armingol2024nrg?). Tools published as a preprint are marked with an asterisk.

Phylogenetic tree of computational tools for inferring cell–cell interactions, from (armingol2024nrg?). Tools published as a preprint are marked with an asterisk.

Personalised medecine applied to Inflammatory Bowel Disease

Steady-state equations

Steady-state results

BioModels: a repository of biological models

BioModels submission flowchart

Conclusion

Take-Aways:

  • BioModels, a data platform for storing curated biological models.
  • However, no automated running of code snippets, nor mandatory access to original data
  • Hard-coded tools, such as COPASI, enable quick analyses for non-expert audience
  • But they’re limited in terms of functionalities and flexibility, to be used with caution.

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Bibliographic References

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License rights

© 2025 Bastien CHASSAGNOL

Opinions expressed are solely my own and do not express the views of the researchers I am associated with.

This work is released under the MIT license.

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